Mitochondrial DNA Research Articles

The genome sequence of a robberfly Leptogaster cylindrica (De Geer, 1776)

We present a genome assembly from an individual female Leptogaster cylindrica (robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence spans 196.60 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,816 protein-coding genes.

The genome sequence of a lichen-forming fungus, Platismatia glauca Linnaeus, 1753

We present a genome assembly from a specimen of Platismatia glauca (lichen-forming fungus; Ascomycota; Lecanoromycetes; Lecanorales; Parmeliaceae). The genome sequence is 33.2 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 95.06 kilobases in length.

The genome sequence of an elaterid beetle, Ctenicera cuprea (Fabricius, 1775)

We present a genome assembly from an individual male elaterid beetle, Ctenicera cuprea (Arthropoda; Insecta; Coleoptera; Elateridae). The genome sequence spans 647.70 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,524 protein-coding genes.

The genome sequence of a hoverfly, Melangyna quadrimaculata (Verrall, 1873)

We present a genome assembly from an individual male Melangyna quadrimaculata (a hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence spans 951.90 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.07 kilobases in length. Gene annotation of this assembly on Ensembl identified 35,607 protein-coding genes.

The genome sequence of a robberfly, Dysmachus trigonus (Meigen, 1804)

We present a genome assembly from an individual male robberfly, Dysmachus trigonus (Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a length of 450.3 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.93 kilobases in length.

The genome sequence of a braconid wasp, Aleiodes leptofemur van Achterberg & Shaw, 2016

We present a genome assembly from an individual male Aleiodes leptofemur (braconid wasp; Arthropoda; Insecta; Hymenoptera; Braconidae). The genome sequence spans 271.20 megabases. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 32.28 kilobases in length.

The genome sequence of the Mottled Beauty moth, Alcis repandata (Linnaeus, 1758)

We present a genome assembly from a female Mottled Beauty moth, Alcis repandata (Arthropoda; Insecta; Lepidoptera; Geometridae). The nuclear genome has a total length of 396.40 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.47 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,231 protein-coding genes.

The genome sequence of the Clouded Brindle moth, Apamea epomidion (Haworth, 1809)

We present a genome assembly from an individual female Apamea epomidion (the Clouded Brindle moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence spans 624.60 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,961 protein-coding genes.

The genome sequence of the acalyptrate fly Dryomyza anilis Fallén, 1820

We present a genome assembly from an individual male acalyptrate fly Dryomyza anilis (Arthropoda; Insecta; Diptera; Dryomyzidae). The genome sequence has a total length of 656.60 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.48 kilobases in length.

The genome sequence of the Small Scabious Mining Bee, Andrena marginata Fabricius, 1776

We present a genome assembly from an individual female Andrena marginata (the Small Scabious Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence spans 373.60 megabases. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.16 kilobases in length.

The genome sequence of the Common Tamarisk-moss, Thuidium tamariscinum (Hedw.) Schimp. (Thuidiaceae)

We present a genome assembly from an individual Thuidium tamariscinum gametophyte (the Common Tamarisk-moss; Streptophyta; Bryopsida; Hypnales; Thuidiaceae). The genome sequence has a length of 363.00 megabases. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 103.12 kilobases and 125.05 kilobases, respectively.

The Mitogenome of the Haecon-5 Strain of Haemonchus contortus and a Comparative Analysis of Its Nucleotide Variation with Other Laboratory Strains.

Haemonchus contortus (the barber's pole worm)-a highly pathogenic gastric nematode of ruminants-causes significant economic losses in the livestock industry worldwide. H. contortus has become a valuable model organism for both fundamental and applied research (e.g., drug and vaccine discovery) because of the availability of well-defined laboratory strains (e.g., MHco3(ISE).N1 in the UK and Haecon-5 in Australia) and genomic, transcriptomic and proteomic data sets. Many recent investigations have relied heavily on the use of the chromosome-contiguous genome of MHco3(ISE).N1 in the absence of a genome for Haecon-5. However, there has been no genetic comparison of these and other strains to date. Here, we assembled and characterised the mitochondrial genome (14.1 kb) of Haecon-5 and compared it with that of MHco3(ISE).N1 and two other strains (i.e., McMaster and NZ_Hco_NP) from Australasia. We detected 276 synonymous and 25 non-synonymous single nucleotide polymorphisms (SNPs) within Haecon-5. Between the Haecon-5 and MHco3(ISE).N1 strains, we recorded 345 SNPs, 31 of which were non-synonymous and linked to fixed amino acid differences in seven protein-coding genes (nad5, nad6, nad1, atp6, nad2, cytb and nad4) between these strains. Pronounced variation (344 and 435 SNPs) was seen between Haecon-5 and each of the other two strains from Australasia. The question remains as to what impact these mitogenomic mutations might have on the biology and physiology of H. contortus, which warrants exploration. The high degree of mitogenomic variability recorded here among these strains suggests that further work should be undertaken to assess the nature and extent of the nuclear genomic variation within H. contortus.

Mfn2R364W, Mfn2G176S, and Mfn2H165R mutations drive Charcot-Marie-Tooth type 2A disease by inducing apoptosis and mitochondrial oxidative phosphorylation damage

Charcot-Marie-Tooth type 2A (CMT2A) is a single-gene motor sensory neuropathy caused by Mfn2 mutation. It is generally believed that CMT2A involves mitochondrial fusion disruption. However, how Mfn2 mutation mediates the mitochondrial membrane fusion loss and its further pathogenic mechanisms remain unclear. Here, in vivo and in vitro mouse models harboring the Mfn2R364W, Mfn2G176S and Mfn2H165R mutations were constructed. Mitochondrial membrane fusion and fission proteins analysis showed that Mfn2R364W, Mfn2G176S, and Mfn2H165R/+ mutations maintain the expression of Mfn2, but promote Drp1 upregulation and Opa1 hydrolytic cleavage. In Mfn2H165R/H165R mutation, Mfn2, Drp1, and Opa1 all play a role in inducing mitochondrial fragmentation, and the mitochondrial aggregation is affected by Mfn2 loss. Further research into the pathogenesis of CMT2A showed these three mutations all induce mitochondria-mediated apoptosis, and mitochondrial oxidative phosphorylation damage. Overall, loss of overall fusion activity affects mitochondrial DNA (mtDNA) stability and causes mitochondrial loss and dysfunction, ultimately leading to CMT2A disease. Interestingly, the differences in the pathogenesis of CMT2A between Mfn2R364W, Mfn2G176S, Mfn2H165R/+ and Mfn2H165R/H165R mutations, including the distribution of Mfn2 and mitochondria, the expression of mitochondrial outer membrane-associated proteins (Bax, VDAC1 and AIF), and the enzyme activity of mitochondrial complex I, are related to the expression of Mfn2.

Larval Taxonomy of the Caddisfly Cernotina truncona Ross, 1947 (Trichoptera: Polycentropodidae)

The genus Cernotina Ross, 1938 is represented in the southeastern United States by three nominal species: Cernotina calcea Ross, 1938, Cernotina spicata Ross, 1938, and Cernotina truncona Ross, 1947. Of all Cernotina species, only the larva of C. spicata has been described to date. The goal of this paper is to describe, illustrate, and diagnose the larva of C. truncona using ecologically associated specimens. In addition, we used publicly available mitochondrial DNA barcoding data to evaluate the genetic relationships of these species. The larvae of Cernotina truncona can be distinguished from those of C. spicata by differences in setal placement and number on the meso- and metanota, mandibular morphology, head width, and distal setation of the tarsi. The ultrastructure of the anal claw is figured, highlighting the novel finding of small spines on the concave margin of a larva of Cernotina. With this new description, just the second described larva from this genus, only C. calcea remains unknown in the southeastern United States. The information provided herein enables the in-depth study of the ecology and life history of this diminutive caddisfly.

Defective mitochondrial COX1 translation due to loss of COX14 function triggers ROS-induced inflammation in mouse liver

Mitochondrial oxidative phosphorylation (OXPHOS) fuels cellular ATP demands. OXPHOS defects lead to severe human disorders with unexplained tissue specific pathologies. Mitochondrial gene expression is essential for OXPHOS biogenesis since core subunits of the complexes are mitochondrial-encoded. COX14 is required for translation of COX1, the central mitochondrial-encoded subunit of complex IV. Here we describe a COX14 mutant mouse corresponding to a patient with complex IV deficiency. COX14M19I mice display broad tissue-specific pathologies. A hallmark phenotype is severe liver inflammation linked to release of mitochondrial RNA into the cytosol sensed by RIG-1 pathway. We find that mitochondrial RNA release is triggered by increased reactive oxygen species production in the deficiency of complex IV. Additionally, we describe a COA3Y72C mouse, affected in an assembly factor that cooperates with COX14 in early COX1 biogenesis, which displays a similar yet milder inflammatory phenotype. Our study provides insight into a link between defective mitochondrial gene expression and tissue-specific inflammation.

Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome.

In mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA delivery factor and report its cryo-electron microscopy structure in complex with SLIRP (SRA stem-loop-interacting RNA-binding protein), mRNA and the mitoribosome. The structure shows that LRPPRC associates with the mitoribosomal proteins mS39 and the N terminus of mS31 through recognition of the LRPPRC helical repeats. Together, the proteins form a corridor for handoff of the mRNA. The mRNA is directly bound to SLIRP, which also has a stabilizing function for LRPPRC. To delineate the effect of LRPPRC on individual mitochondrial transcripts, we used RNA sequencing, metabolic labeling and mitoribosome profiling, which showed a transcript-specific influence on mRNA translation efficiency, with cyclooxygenase 1 and 2 translation being the most affected. Our data suggest that LRPPRC-SLIRP acts in recruitment of mitochondrial mRNAs to modulate their translation. Collectively, the data define LRPPRC-SLIRP as a regulator of the mitochondrial gene expression system.

The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis.

The Ylistrum japonicum is a commercially valuable scallop known for its long-distance swimming abilities. Despite its economic importance, genetic and genomic research on this species is limited. This study presents the first complete mitochondrial genome of Y. japonicum. The mitochondrial genome is 19,475 bp long and encompasses 13 protein-coding genes, three ribosomal RNA genes, and 23 transfer RNA genes. Two distinct phylogenetic analyses were used to explore the phylogenetic position of the Y. japonicum within the family Pectinidae. Based on one mitochondrial phylogenetic analysis by selecting 15 Pectinidae species and additional outgroup taxa and one single gene phylogenetic analysis by 16S rRNA, two phylogenetic trees were constructed to provide clearer insights into the evolutionary placement of Y. japonicum within the family Pectinidae. Our analysis reveals that Ylistrum is a basal lineage to the Pectininae clade, distinct from its previously assigned tribe, Amusiini. This study offers critical insights into the genetic makeup and evolutionary history of Y. japonicum, enhancing our knowledge of this economically vital species.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Triplophysa microphthalma.

The complete mitochondrial genome has been extensively utilized in studies related to phylogenetics, offering valuable perspectives on evolutionary relationships. The mitochondrial genome of the fine-eyed plateau loach, Triplophysa microphthalma, has not attracted much attention, although this species is endemic to China. In this study, we characterized the mitochondrial genome of T. microphthalma and reassessed the classification status of its genus. The complete mitochondrial genome of T. microphthalma was 16,591 bp and contained thirty-seven genes, including thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and twenty-two transfer RNA genes (tRNAs). All but one of the thirteen PCGs had the regular start codon ATG; the gene cox1 started with GTG. Six PCGs had incomplete stop codons (T--). These thirteen PCGs are thought to have evolved under purifying selection, and the mitogenome shared a high degree of similarity with the genomes of species within the genus Leptobotia. All tRNA genes exhibited the standard clover-shaped structure, with the exception of the trnS1 gene, which lacked a DHU stem. A phylogenetic analysis indicated that T. microphthalma was more closely related to species within the genus Triplophysa than to those in Barbatula. The present study contributes valuable genomic information for T. microphthalma, and offers new perspectives on the phylogenetic relationships among species of Triplophysa and Barbatula. The findings also provide essential data that can inform the management and conservation strategies for T. microphthalma and other species of Triplophysa and Barbatula.

Inhibition of angiogenesis by the secretome from iPSC-derived retinal ganglion cells with Leber's hereditary optic neuropathy-like phenotypes

The blood supply in the retina ensures photoreceptor function and maintains regular vision. Leber's hereditary optic neuropathy (LHON), caused by the mitochondrial DNA mutations that deteriorate complex I activity, is characterized by progressive vision loss. Although some reports indicated retinal vasculature abnormalities as one of the comorbidities in LHON, the paracrine influence of LHON-affected retinal ganglion cells (RGCs) on vascular endothelial cell physiology remains unclear. To address this, we established an in vitro model of mitochondrial complex I deficiency using induced pluripotent stem cell-derived RGCs (iPSC-RGCs) treated with a mitochondrial complex I inhibitor rotenone (Rot) to recapitulate LHON pathologies. The secretomes from Rot-treated iPSC-RGCs (Rot-iPSC-RGCs) were collected, and their treatment effect on human umbilical vein endothelial cells (HUVECs) was studied. Rot induced LHON-like characteristics in iPSC-RGCs, including decreased mitochondrial complex I activity and membrane potential, and increased mitochondrial reactive oxygen species (ROS) and apoptosis, leading to mitochondrial dysfunction. When HUVECs were exposed to conditioned media (CM) from Rot-iPSC-RGCs, the angiogenesis of HUVECs was suppressed compared to those treated with CM from control iPSC-RGCs (Ctrl-iPSC-RGCs). Angiogenesis-related proteins were altered in the secretomes from Rot-iPSC-RGC-derived CM, particularly angiopoietin, MMP-9, uPA, collagen XVIII, and VEGF were reduced. Notably, GeneMANIA analysis indicated that VEGFA emerged as the pivotal angiogenesis-related protein among the identified proteins secreted by health iPSC-RGCs but reduced in the secretomes from Rot-iPSC-RGCs. Quantitative real-time PCR and western blots confirmed the reduction of VEGFA at both transcription and translation levels, respectively. Our study reveals that Rot-iPSC-RGCs establish a microenvironment to diminish the angiogenic potential of vascular cells nearby, shedding light on the paracrine regulation of LHON-affected RGCs on retinal vasculature.

Paternal Mitochondrial DNA Leakage in Natural Populations of Large-Scale Loach, Paramisgurnus dabryanus.

Animal mitochondrial DNA is usually considered to comply with strict maternal inheritance, and only one mitochondrial DNA haplotype exists in an individual. However, mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype, has recently been reported in some animals, such as mice, mussels, and birds. This study conducted extensive field surveys to obtain representative samples to investigate the existence of paternal inheritance of mitochondrial DNA (mtDNA) in natural fish populations. Evidence of paternal mitochondrial DNA leakage of P. dabryanus was discovered using high-throughput sequencing and bioinformatics methods. Two distinct mitochondrial haplotypes (16,569 bp for haplotype I and 16,646 bp for haplotype II) were observed, differing by 18.83% in nucleotide sequence. Phylogenetic analysis suggests divergence between these haplotypes and potential interspecific hybridization with M. anguillicaudatus, leading to paternal leakage. In natural populations of P. dabryanus along the Yangtze River, both haplotypes are present, with Type I being dominant (75% copy number). Expression analysis shows that Type I has higher expression levels of ND3 and ND6 genes compared to Type II, suggesting Type I's primary role. This discovery of a species with two mitochondrial types provides a model for studying paternal leakage heterogeneity and insights into mitochondrial genome evolution and inheritance.